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Abstract:

The IPPP-CLOPPA method is applied to investigate the influence of a methyl group on the energy of the hydrogen bonds and the potential energy curve of the bridge protons in model compounds, which mimic the methylated and unmethylated cytosine-guanine base pairs. On the same grounds, this influence on the polarizability of the intermolecular hydrogen bonds of these compounds is also addressed, in order to determine whether this linear response property provides a significant proof of the electronic mechanisms that affect the stabilization of the hydrogen bonds. Results obtained show that the methyl electronic system delocalizes on the hydrogen bond region, and changes of these intermolecular hydrogen bonds are due to this effect of delocalization. © 2017 American Chemical Society.

Registro:

Documento: Artículo
Título:IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair
Autor:Giribet, C.G.; Ruiz De Azúa, M.C.
Filiación:Facultad de Ciencias Exactas y Naturales, Departamento de Física, Universidad de Buenos Aires, Buenos Aires, 1428, Argentina
Instituto de Física de Buenos Aires (IFIBA), CONICET, Universidad de Buenos Aires, Buenos Aires, 1428, Argentina
Palabras clave:Alkylation; Complexation; Molecular physics; Polarization; Positive ions; Potential energy; Delocalizations; Electronic mechanisms; Electronic systems; Intermolecular hydrogen bonds; Linear response; Molecular polarizabilities; Polarizabilities; Potential energy curves; Hydrogen bonds; cytosine; guanine; base pairing; chemistry; hydrogen bond; methylation; quantum theory; Base Pairing; Cytosine; Guanine; Hydrogen Bonding; Methylation; Quantum Theory
Año:2017
Volumen:121
Número:15
Página de inicio:2960
Página de fin:2970
DOI: http://dx.doi.org/10.1021/acs.jpca.6b10059
Título revista:Journal of Physical Chemistry A
Título revista abreviado:J Phys Chem A
ISSN:10895639
CODEN:JPCAF
CAS:cytosine, 71-30-7; guanine, 69257-39-2, 73-40-5; Cytosine; Guanine
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_10895639_v121_n15_p2960_Giribet

Referencias:

  • Ebrahimi, A., Habibi Khorassani, S.M., Delarami, H., Esmaeeli, H., The Effect of CH3, F and NO2 Substituents on the Individual Hydrogen Bond Energies in the Adenine-Thymine and Guanine-Cytosine Base Pairs (2010) J. Comput.-Aided Mol. Des., 24, pp. 409-416
  • Clementi, E., Mehl, J., Von Niessen, W., Study of the Electronic Structure of Molecules. XII. Hydrogen Bridges in the Guanine-Cytosine Pair and in the Dimeric Form of Formic Acid (1971) J. Chem. Phys., 54, p. 508
  • Rein, R., Harris, F.E., Studies of Hydrogen-Bonded Systems. I. the Electronic Structure and the Double Well Potential of the N-H. ·n Hydrogen Bond of the Guanine-Cytosine Base Pair (1964) J. Chem. Phys., 41, p. 3393
  • Löwdin, P.-O., Proton Tunneling in DNA and its Biological Implications (1963) Rev. Mod. Phys., 35, p. 724
  • Vanyushin, B.F., Enzymatic DNA Methylation is an Epigenetic Control for Genetic Functions of the Cell (2005) Biochemistry (Moscow), 70, pp. 488-499
  • Vanyushin, B.F., A View of an Elemental Naturalist at the DNA World (Base Composition, Sequences, Methylation) (2007) Biochemistry (Moscow), 72, pp. 1289-1298
  • Forde, G., Flood, A., Salter, L., Hill, G., Gorb, L., Leszczynski, J., Theoretical ab Initio Study of the Effects of Methylation on Structure and Stability of G:C Watson-Crick Base Pair (2003) J. Biomol. Struct. Dyn., 20, pp. 811-817
  • Si, X., Zhao, Y., Yang, C., Zhang, S., Zhang, X., DNA Methylation as a Potential Diagnosis Indicator for Rapid Discrimination of Rare Cancer Cells and Normal Cells (2015) Sci. Rep., 5, p. 11882
  • Song, Q., Qiu, Z., Wang, H., Xia, Y., Shen, J., Zhang, Y., The Effect of Methylation on the Hydrogen-Bonding and Stacking Interaction of Nucleic Acid Bases (2013) Struct. Chem., 24, pp. 55-65
  • Phillips, T., The Role of Methylation in Gene Expression (2008) Nature Education, 1, pp. 116-121
  • Dantas Machado, A.C., Zhou, T., Rao, S., Goel, P., Rastogi, C., Lazarovici, A., Bussemaker, H.J., Rohs, R., Evolving Insights on How Cytosine Methylation Affects Protein-DNA Binding (2015) Briefings Funct. Genomics, 14, pp. 1-13
  • Severin, P.M.D., Zou, X., Gaub, H.E., Schulten, K., Cytosine Methylation Alters DNA Mechanical Properties (2011) Nucleic Acids Res., 39, pp. 8740-8751
  • Demokan, S., Dalay, N., Role of DNA Methylation in Head and Neck Cancer (2011) Clin. Epigenet., 2, pp. 123-150
  • Thienpont, B., Steinbacher, J., Zhao, H., D'Anna, F., Kuchnio, A., Ploumakis, A., Ghesquière, B., Lambrechts, D., Tumour Hypoxia Causes DNA Hypermethylation by Reducing TET Activity (2016) Nature, 537, pp. 63-68
  • Bergman, Y., Cedar, H., DNA Methylation Dynamics in Health and Disease (2013) Nat. Struct. Mol. Biol., 20, pp. 274-281
  • Mirsaidov, U., Timp, W., Zou, X., Dimitrov, V., Schulten, K., Feinberg, A.P., Timp, G., Nanoelectromechanics of Methylated DNA in a Synthetic Nanopore (2009) Biophys. J., 96, pp. 32-34
  • Moser, A., Guza, R., Tretyakova, R., York, D.M., Density Functional Study of the Influence of C5 Cytosine Substitution in Base Pairs with Guanine (2009) Theor. Chem. Acc., 122, pp. 179-188
  • Yusufaly, T.I., Li, Y., Olson, W.K., 5-Methylation of Cytosine in CG:CG Base-pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics (2013) J. Phys. Chem. B, 117, pp. 16436-16442
  • Flood, A., Hubbard, C., Forde, G., Hill, G., Gorb, L., Leszczynski, J., Theoretical Ab Initio Study of the Effects of Methylation on the Nature of Hydrogen Bonding in A:T Base Pair (2003) J. Biomol. Struct. Dyn., 21, pp. 297-302
  • Sponer, J., Leszczynski, J., Hobza, P., Electronic Properties, Hydrogen Bonding, Stacking, and Cation Binding of DNA and RNA Bases (2001) Biopolymers, 61, pp. 3-31
  • Sponer, J., Jurecka, P., Hobza, P., Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs (2004) J. Am. Chem. Soc., 126, pp. 10142-10151
  • Smith, Q.A., Gordon, M.S., Slipchenko, L.V., Effective Fragment Potential Study of the Interaction of DNA Bases (2011) J. Phys. Chem. A, 115, pp. 11269-11276
  • Giribet, C.G., Ruiz De Azúa, M.C., CLOPPA Analysis of the Molecular Polarizability and the Energy of Strong Intramolecular Hydrogen Bonds: Resonance Assisted? (2012) J. Phys. Chem. A, 116, pp. 12175-12183
  • Xiao, S., Wang, L., Liu, Y., Lin, X., Liang, H., Theoretical Investigation of the Proton Transfer Mechanism in Guanine-Cytosine and Adenine-Thymine Base Pairs (2012) J. Chem. Phys., 137, pp. 195101-195108
  • Sowers, L.C., Shaw, B.R., Sedwick, W.D., Base Stacking and Molecular Polarizability: Effect of a Methyl Group in the 5-Position of Pyrimidines (1987) Biochem. Biophys. Res. Commun., 148, pp. 790-794
  • Giribet, C.G., Demarco, M.D., Ruiz De Azúa, M.C., Contreras, R.H., Ab-initio CLOPPA Decomposition of the Static Molecular Polarizability Tensor (1997) Mol. Phys., 91, pp. 105-112
  • Botek, E.L., Giribet, C.G., Ruiz De Azúa, M.C., Negri, R.M., Bernik, D., Evaluation of the Molecular Polarizability Using the IPPP-CLOPPA-INDO/S Method. Application to Molecules of Biological Interest (2008) J. Phys. Chem. A, 112, pp. 6992-6998
  • Giribet, C.G., Ruiz De Azúa, M.C., CLOPPA-IPPP Analysis of Cooperative Effects in H-bonded Molecular Complexes.2. Application to the Static Molecular Polarizability Tensor (2010) J. Phys. Chem. A, 114, pp. 1109-1117
  • Ruiz De Azúa, M.C., Diz, A.C., Giribet, C.G., Contreras, R.H., Rae, I.D., A Polarization Propagator Analysis of Through-Space Spin-Spin Coupling Constants: F-F Couplings (1986) Int. J. Quantum Chem., 30, pp. 585-601
  • Diz, A.C., Giribet, C.G., Ruiz De Azúa, M.C., Contreras, R.H., The Use of Localized Molecular Orbitals and the Polarization Propagator Approach to Identify Transmission Mechanisms in Nuclear Spin-Spin Couplings (1990) Int. J. Quantum Chem., 37, pp. 663-677
  • Ruiz De Azúa, M.C., Giribet, C.G., Vizioli, C.V., Contreras, R.H., Ab-initio IPPP-CLOPPA Approach to Perform Bond Contribution Analysis of NMR Coupling Constants: 1J(NH) in NH3 as a Function of Pyramidality (1998) J. Mol. Struct.: THEOCHEM, 433, pp. 141-150
  • Giribet, C.G., Ruiz De Azúa, M.C., Vizioli, C.V., Cavasotto, C.N., Electronic Mechanisms of Intra and Intermolecular J Couplings in Systems with C-H⋯O Interactions (2003) Int. J. Mol. Sci., 4, pp. 203-217
  • Contreras, R.H., Peralta, J.E., Giribet, C.G., Ruiz De Azúa, M.C., Facelli, J.C., Advances in Theoretical and Physical Aspects of Spin-Spin Coupling Constants (2000) Annual Reports on NMR Spectroscopy, 41, pp. 57-166. , In, Elsevier Inc. London/San Diego
  • Giribet, C.G., Ruiz De Azúa, M.C., CLOPPA-IPPP Analysis of Electronic Mechanisms of Intermolecular 1hJ(A,H) and 2hJ(A,D) Spin-Spin Coupling Constants in Systems with D-H⋯A Hydrogen Bonds (2005) J. Phys. Chem. A, 109, pp. 11980-11988
  • Giribet, C.G., Ruiz De Azúa, M.C., The Sign and Magnitude of 2hJ(F,F) and 1hJ(F,H) in FH⋯FH. A CLOPPA Analysis of their Distance Dependence (2006) J. Phys. Chem. A, 110, pp. 11575-11583
  • Giribet, C.G., Ruiz De Azúa, M.C., CLOPPA-IPPP Analysis of Cooperative Effects in H-bonded Molecular Complexes. Application to Intermolecular 2hJ(N,C) Spin-Spin Coupling Constants in Linear (CNH)n Complexes (2008) J. Phys. Chem. A, 112, pp. 4386-4393
  • Jørgensen, P., Simons, J., (1981) Second Quantization Based Methods in Quantum Chemistry, , Academic Press: London
  • Aidas, K., Angeli, C., Bak, K.L., Bakken, V., Bast, R., Boman, L., Christiansen, O., Ågren, H., ″the Dalton quantum chemistry program system″ (2014) WIREs Comput. Mol. Sci., 4, pp. 269-284
  • Van Duijneveldt-Van De Rijdt, J.G.C.M., Van Duijneveldt, F.B., (1971) J. Am. Chem. Soc., 93, p. 5644
  • Lazzeretti, P., Zanasi, R., Anisotropy of the Nuclear Spin-Spin Coupling Tensor in Water, Ammonia, and Methane Molecules (1982) J. Chem. Phys., 77, pp. 2448-2453
  • Lazzeretti, P., Geometric Approximation to Nuclear Spin-Spin Coupling Constants in the Water Molecule (1979) Int. J. Quantum Chem., 15, pp. 181-196
  • Lazzeretti, P., Calculation of Nuclear Spin-Spin Coupling Constants in Methanol Molecule (1979) J. Chem. Phys., 71, pp. 2514-2521
  • Jørgensen, P., Simons, J., (1981) Second Quantization-based Methods in Quantum Chemistry, , Academic Press: London
  • Gilli, P., Bertolasi, V., Ferretti, V., Gilli, G., Evidence for Intramolecular N-H⋯O Resonance-Assisted Hydrogen Bonding in β-Enaminones and Related Heterodienes. A Combined Crystal-Structural, IR and NMR Spectroscopic, and Quantum-Mechanical Investigation (2000) J. Am. Chem. Soc., 122, pp. 10405-10417

Citas:

---------- APA ----------
Giribet, C.G. & Ruiz De Azúa, M.C. (2017) . IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair. Journal of Physical Chemistry A, 121(15), 2960-2970.
http://dx.doi.org/10.1021/acs.jpca.6b10059
---------- CHICAGO ----------
Giribet, C.G., Ruiz De Azúa, M.C. "IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair" . Journal of Physical Chemistry A 121, no. 15 (2017) : 2960-2970.
http://dx.doi.org/10.1021/acs.jpca.6b10059
---------- MLA ----------
Giribet, C.G., Ruiz De Azúa, M.C. "IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair" . Journal of Physical Chemistry A, vol. 121, no. 15, 2017, pp. 2960-2970.
http://dx.doi.org/10.1021/acs.jpca.6b10059
---------- VANCOUVER ----------
Giribet, C.G., Ruiz De Azúa, M.C. IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair. J Phys Chem A. 2017;121(15):2960-2970.
http://dx.doi.org/10.1021/acs.jpca.6b10059